How to improve the accuracy for a rigid bodies
Work smart, not ...

Okay, so you realized Blender bullet solver implementation is not as strong out of the box. Therefore we have to help it out a bit.


Reconstruct your geometry with simpler shapes. In your specific file, I could just create the crate out of 5 cubes (the walls and floor) which are then parented to the crate geometry.

Use simple rigid body shape wherever possible. I made the walls into Box colliders and the sphere into Sphere colliders.


Now, you realized, that the Steps per Second and Solver Iterations don't ensure a more stable simulation, if we just increase them. Here comes a workaround: We'll make our subframes into actual frames by slowing down the simulation and the speeding it up afterwards.


Scale the keyframes apart by 6. The box now moves 6 times as slow.
Adjust the speed of the rigid body simulation. I entered 1.0/6.

Adjust the playback speed. The fps will be 24*6 and the render steps can be 6. (Obviously the scene's end will have to be adjusted as well.)

Increase the Solver steps and Iterations as needed. I used [500, 500], as shown in the above image.


The resulting simulation is stable, although my computer can't playback a 144 fps.